GROMACS version: 2020
GROMACS modification: No
Hello all,
I wonder how to calculate the histogram (binning) of the hydrogen bonds? Something similar to what the gmx density -number does for counting the atom’s population according the x, y, z.
I am just not sure how close is what the gmx hbond -hbm gives as a map to what I desire.
Thank you
Hi,
gmx hbond -hbm provides a xpm map having in x the simulation time and y the index number of hydrogen bond. The map tells you if you have or not a specific hydrogen bond at that specific point in time.
Is this what you want?
Best regards
Alessandra
Hi,
Thanks.
Then it seems that the gmx hbond -hbm does not directly give what I am looking for. I am interested in the spatial (x,y,z) distribution of the hydrogen bonds, so that I would be able to count numerically that how many hydrogen bonds exist in a bin such as \Delta \text{x} \times \Delta \text{y} \times \Delta \text{z}.
So, any comment is greatly appreciated.
Regards